Starting phenix.real_space_refine on Sun Jun 29 03:54:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5uk1_8563/06_2025/5uk1_8563_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5uk1_8563/06_2025/5uk1_8563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5uk1_8563/06_2025/5uk1_8563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5uk1_8563/06_2025/5uk1_8563.map" model { file = "/net/cci-nas-00/data/ceres_data/5uk1_8563/06_2025/5uk1_8563_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5uk1_8563/06_2025/5uk1_8563_trim.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.069 sd= 0.375 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 75 5.16 5 C 11004 2.51 5 N 2985 2.21 5 O 3483 1.98 5 H 16401 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33948 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "B" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "C" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "D" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "E" Number of atoms: 4973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 4973 Classifications: {'peptide': 323} Link IDs: {'PTRANS': 20, 'TRANS': 302} Chain: "F" Number of atoms: 2716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 2716 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "G" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "H" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "I" Number of atoms: 3476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3476 Classifications: {'peptide': 236} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 225} Chain breaks: 1 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 16.47, per 1000 atoms: 0.49 Number of scatterers: 33948 At special positions: 0 Unit cell: (141.04, 129.56, 182.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 O 3483 8.00 N 2985 7.00 C 11004 6.00 H 16401 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS B 637 " distance=2.05 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 278 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 71 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 306 " distance=2.02 Simple disulfide: pdb=" SG CYS B 644 " - pdb=" SG CYS B 648 " distance=2.03 Simple disulfide: pdb=" SG CYS C 8 " - pdb=" SG CYS D 637 " distance=1.96 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 278 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 71 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 306 " distance=2.02 Simple disulfide: pdb=" SG CYS D 644 " - pdb=" SG CYS D 648 " distance=2.03 Simple disulfide: pdb=" SG CYS E 8 " - pdb=" SG CYS F 637 " distance=2.06 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 278 " distance=2.03 Simple disulfide: pdb=" SG CYS E 59 " - pdb=" SG CYS E 71 " distance=2.04 Simple disulfide: pdb=" SG CYS E 94 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 282 " - pdb=" SG CYS E 306 " distance=2.02 Simple disulfide: pdb=" SG CYS F 644 " - pdb=" SG CYS F 648 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 406 " - " ASN A 129 " " NAG A 407 " - " ASN A 163 " " NAG A 408 " - " ASN A 15 " " NAG A 409 " - " ASN A 27 " " NAG A 410 " - " ASN A 290 " " NAG B 701 " - " ASN B 654 " " NAG C 406 " - " ASN C 129 " " NAG C 407 " - " ASN C 163 " " NAG C 408 " - " ASN C 15 " " NAG C 409 " - " ASN C 27 " " NAG C 410 " - " ASN C 290 " " NAG D 701 " - " ASN D 654 " " NAG E 406 " - " ASN E 129 " " NAG E 407 " - " ASN E 163 " " NAG E 408 " - " ASN E 15 " " NAG E 409 " - " ASN E 27 " " NAG E 410 " - " ASN E 290 " " NAG F 701 " - " ASN F 654 " " NAG J 1 " - " ASN A 91 " " NAG K 1 " - " ASN A 58 " " NAG L 1 " - " ASN C 91 " " NAG M 1 " - " ASN C 58 " " NAG N 1 " - " ASN E 91 " " NAG O 1 " - " ASN E 58 " Time building additional restraints: 8.60 Conformation dependent library (CDL) restraints added in 2.7 seconds 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 48 sheets defined 18.4% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.63 Creating SS restraints... Processing helix chain 'A' and resid 60 through 67 removed outlier: 4.083A pdb=" N GLY A 67 " --> pdb=" O GLY A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 109 Processing helix chain 'A' and resid 122 through 127 removed outlier: 4.166A pdb=" N TRP A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.994A pdb=" N GLN A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 557 Processing helix chain 'B' and resid 574 through 626 removed outlier: 3.803A pdb=" N GLN B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU B 626 " --> pdb=" O VAL B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 654 Processing helix chain 'B' and resid 662 through 670 Processing helix chain 'C' and resid 60 through 67 removed outlier: 4.084A pdb=" N GLY C 67 " --> pdb=" O GLY C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 109 Processing helix chain 'C' and resid 122 through 127 removed outlier: 4.166A pdb=" N TRP C 127 " --> pdb=" O LYS C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 195 removed outlier: 3.995A pdb=" N GLN C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 557 Processing helix chain 'D' and resid 574 through 626 removed outlier: 3.802A pdb=" N GLN D 625 " --> pdb=" O LYS D 621 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 626 " --> pdb=" O VAL D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 654 Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'E' and resid 60 through 67 removed outlier: 4.084A pdb=" N GLY E 67 " --> pdb=" O GLY E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 109 Processing helix chain 'E' and resid 122 through 127 removed outlier: 4.166A pdb=" N TRP E 127 " --> pdb=" O LYS E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 195 removed outlier: 3.994A pdb=" N GLN E 191 " --> pdb=" O ASN E 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 557 Processing helix chain 'F' and resid 574 through 626 removed outlier: 3.803A pdb=" N GLN F 625 " --> pdb=" O LYS F 621 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU F 626 " --> pdb=" O VAL F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 654 Processing helix chain 'F' and resid 662 through 670 Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.535A pdb=" N PHE G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.534A pdb=" N PHE H 84 " --> pdb=" O PRO H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.534A pdb=" N PHE I 84 " --> pdb=" O PRO I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 215 Processing sheet with id=AA1, first strand: chain 'B' and resid 531 through 536 removed outlier: 3.990A pdb=" N CYS B 637 " --> pdb=" O ILE B 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 48 removed outlier: 5.917A pdb=" N LEU A 47 " --> pdb=" O ALA A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.601A pdb=" N LEU A 54 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA7, first strand: chain 'A' and resid 136 through 140 removed outlier: 4.706A pdb=" N CYS A 139 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 151 through 153 removed outlier: 8.152A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 151 through 153 removed outlier: 8.152A pdb=" N LEU A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 289 removed outlier: 3.921A pdb=" N CYS A 282 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 531 through 536 removed outlier: 3.990A pdb=" N CYS D 637 " --> pdb=" O ILE D 633 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 21 through 22 Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AB6, first strand: chain 'C' and resid 47 through 48 removed outlier: 5.916A pdb=" N LEU C 47 " --> pdb=" O ALA C 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 54 through 55 removed outlier: 6.601A pdb=" N LEU C 54 " --> pdb=" O VAL C 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AB9, first strand: chain 'C' and resid 136 through 140 removed outlier: 4.706A pdb=" N CYS C 139 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC4, first strand: chain 'C' and resid 287 through 289 removed outlier: 3.921A pdb=" N CYS C 282 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 531 through 536 removed outlier: 3.990A pdb=" N CYS F 637 " --> pdb=" O ILE F 633 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 21 through 22 Processing sheet with id=AC7, first strand: chain 'E' and resid 33 through 35 Processing sheet with id=AC8, first strand: chain 'E' and resid 47 through 48 removed outlier: 5.916A pdb=" N LEU E 47 " --> pdb=" O ALA E 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.602A pdb=" N LEU E 54 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD2, first strand: chain 'E' and resid 136 through 140 removed outlier: 4.707A pdb=" N CYS E 139 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 151 through 153 removed outlier: 8.151A pdb=" N LEU E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD6, first strand: chain 'E' and resid 287 through 289 removed outlier: 3.922A pdb=" N CYS E 282 " --> pdb=" O ILE E 289 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN G 38 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU G 47 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 10 through 13 Processing sheet with id=AE1, first strand: chain 'G' and resid 129 through 132 removed outlier: 5.809A pdb=" N GLY G 141 " --> pdb=" O ASN G 209 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 136 through 137 removed outlier: 6.991A pdb=" N MET G 159 " --> pdb=" O GLY G 175 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY G 175 " --> pdb=" O MET G 159 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP G 161 " --> pdb=" O VAL G 173 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE4, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN H 38 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N LEU H 47 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 13 Processing sheet with id=AE6, first strand: chain 'H' and resid 129 through 132 removed outlier: 5.810A pdb=" N GLY H 141 " --> pdb=" O ASN H 209 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 136 through 137 removed outlier: 6.992A pdb=" N MET H 159 " --> pdb=" O GLY H 175 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLY H 175 " --> pdb=" O MET H 159 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP H 161 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 4 through 5 Processing sheet with id=AE9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.264A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AF2, first strand: chain 'I' and resid 129 through 132 removed outlier: 5.809A pdb=" N GLY I 141 " --> pdb=" O ASN I 209 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 136 through 137 removed outlier: 6.991A pdb=" N MET I 159 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLY I 175 " --> pdb=" O MET I 159 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP I 161 " --> pdb=" O VAL I 173 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.28 Time building geometry restraints manager: 10.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.01: 16395 1.01 - 1.21: 6 1.21 - 1.42: 7627 1.42 - 1.62: 10214 1.62 - 1.82: 102 Bond restraints: 34344 Sorted by residual: bond pdb=" CA TRP I 36 " pdb=" CB TRP I 36 " ideal model delta sigma weight residual 1.532 1.483 0.048 1.82e-02 3.02e+03 7.03e+00 bond pdb=" CA TRP H 36 " pdb=" CB TRP H 36 " ideal model delta sigma weight residual 1.532 1.484 0.048 1.82e-02 3.02e+03 6.87e+00 bond pdb=" CA TRP G 36 " pdb=" CB TRP G 36 " ideal model delta sigma weight residual 1.532 1.484 0.047 1.82e-02 3.02e+03 6.80e+00 bond pdb=" NE1 TRP C 153 " pdb=" HE1 TRP C 153 " ideal model delta sigma weight residual 0.860 0.809 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" NE1 TRP A 153 " pdb=" HE1 TRP A 153 " ideal model delta sigma weight residual 0.860 0.810 0.050 2.00e-02 2.50e+03 6.34e+00 ... (remaining 34339 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 55733 2.10 - 4.20: 5029 4.20 - 6.30: 665 6.30 - 8.40: 108 8.40 - 10.51: 22 Bond angle restraints: 61557 Sorted by residual: angle pdb=" C GLU I 1 " pdb=" N ILE I 2 " pdb=" CA ILE I 2 " ideal model delta sigma weight residual 120.35 127.76 -7.41 1.39e+00 5.18e-01 2.84e+01 angle pdb=" C GLU G 1 " pdb=" N ILE G 2 " pdb=" CA ILE G 2 " ideal model delta sigma weight residual 120.35 127.73 -7.38 1.39e+00 5.18e-01 2.82e+01 angle pdb=" C GLU H 1 " pdb=" N ILE H 2 " pdb=" CA ILE H 2 " ideal model delta sigma weight residual 120.35 127.69 -7.34 1.39e+00 5.18e-01 2.79e+01 angle pdb=" N SER H 30 " pdb=" CA SER H 30 " pdb=" C SER H 30 " ideal model delta sigma weight residual 113.28 121.54 -8.26 1.57e+00 4.06e-01 2.77e+01 angle pdb=" N SER I 30 " pdb=" CA SER I 30 " pdb=" C SER I 30 " ideal model delta sigma weight residual 113.28 121.53 -8.25 1.57e+00 4.06e-01 2.76e+01 ... (remaining 61552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.35: 15607 19.35 - 38.71: 867 38.71 - 58.06: 271 58.06 - 77.42: 46 77.42 - 96.77: 15 Dihedral angle restraints: 16806 sinusoidal: 9345 harmonic: 7461 Sorted by residual: dihedral pdb=" CA GLY I 58 " pdb=" C GLY I 58 " pdb=" N ILE I 59 " pdb=" CA ILE I 59 " ideal model delta harmonic sigma weight residual -180.00 -147.43 -32.57 0 5.00e+00 4.00e-02 4.24e+01 dihedral pdb=" CA GLY H 58 " pdb=" C GLY H 58 " pdb=" N ILE H 59 " pdb=" CA ILE H 59 " ideal model delta harmonic sigma weight residual -180.00 -147.47 -32.53 0 5.00e+00 4.00e-02 4.23e+01 dihedral pdb=" CA GLY G 58 " pdb=" C GLY G 58 " pdb=" N ILE G 59 " pdb=" CA ILE G 59 " ideal model delta harmonic sigma weight residual -180.00 -147.51 -32.49 0 5.00e+00 4.00e-02 4.22e+01 ... (remaining 16803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2235 0.081 - 0.163: 398 0.163 - 0.244: 43 0.244 - 0.326: 11 0.326 - 0.407: 7 Chirality restraints: 2694 Sorted by residual: chirality pdb=" C1 BMA L 3 " pdb=" O4 NAG L 2 " pdb=" C2 BMA L 3 " pdb=" O5 BMA L 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.76e+01 chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.66e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.53e+01 ... (remaining 2691 not shown) Planarity restraints: 5244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 248 " -0.149 2.00e-02 2.50e+03 1.75e-01 4.60e+02 pdb=" CG ASN E 248 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN E 248 " 0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN E 248 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN E 248 " 0.260 2.00e-02 2.50e+03 pdb="HD22 ASN E 248 " -0.263 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 248 " -0.148 2.00e-02 2.50e+03 1.74e-01 4.56e+02 pdb=" CG ASN A 248 " -0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 248 " 0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN A 248 " 0.003 2.00e-02 2.50e+03 pdb="HD21 ASN A 248 " 0.259 2.00e-02 2.50e+03 pdb="HD22 ASN A 248 " -0.262 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 248 " 0.148 2.00e-02 2.50e+03 1.74e-01 4.53e+02 pdb=" CG ASN C 248 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 248 " -0.157 2.00e-02 2.50e+03 pdb=" ND2 ASN C 248 " -0.003 2.00e-02 2.50e+03 pdb="HD21 ASN C 248 " -0.258 2.00e-02 2.50e+03 pdb="HD22 ASN C 248 " 0.261 2.00e-02 2.50e+03 ... (remaining 5241 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.31: 7614 2.31 - 2.88: 77229 2.88 - 3.45: 86327 3.45 - 4.03: 119135 4.03 - 4.60: 178874 Nonbonded interactions: 469179 Sorted by model distance: nonbonded pdb=" H GLY H 140 " pdb=" O LEU H 210 " model vdw 1.735 2.450 nonbonded pdb=" H THR E 31 " pdb=" O LEU E 321 " model vdw 1.736 2.450 nonbonded pdb=" H THR C 31 " pdb=" O LEU C 321 " model vdw 1.736 2.450 nonbonded pdb=" H THR A 31 " pdb=" O LEU A 321 " model vdw 1.737 2.450 nonbonded pdb=" H GLY G 140 " pdb=" O LEU G 210 " model vdw 1.738 2.450 ... (remaining 469174 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.13 Found NCS groups: ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } Set up NCS constraints Number of NCS constrained groups: 5 pdb_interpretation.ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'O' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'H' } pdb_interpretation.ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.680 Extract box with map and model: 1.140 Check model and map are aligned: 0.230 Set scattering table: 0.270 Process input model: 74.950 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.020 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.083 17997 Z= 0.467 Angle : 1.305 9.783 24459 Z= 0.751 Chirality : 0.065 0.407 2694 Planarity : 0.009 0.082 3132 Dihedral : 12.045 96.773 7023 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.06 % Favored : 91.80 % Rotamer: Outliers : 0.16 % Allowed : 1.13 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.14), residues: 2172 helix: -1.38 (0.22), residues: 348 sheet: -2.97 (0.17), residues: 546 loop : -2.94 (0.14), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.005 TRP A 127 HIS 0.019 0.005 HIS D 611 PHE 0.036 0.004 PHE D 509 TYR 0.032 0.005 TYR C 95 ARG 0.026 0.002 ARG H 222 Details of bonding type rmsd link_NAG-ASN : bond 0.01180 ( 24) link_NAG-ASN : angle 3.93090 ( 72) link_BETA1-4 : bond 0.01125 ( 9) link_BETA1-4 : angle 4.08142 ( 27) hydrogen bonds : bond 0.10955 ( 654) hydrogen bonds : angle 11.13390 ( 1845) SS BOND : bond 0.01864 ( 21) SS BOND : angle 2.19512 ( 42) covalent geometry : bond 0.01011 (17943) covalent geometry : angle 1.28106 (24318) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4344 Ramachandran restraints generated. 2172 Oldfield, 0 Emsley, 2172 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 78 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.9504 (tp40) cc_final: 0.9098 (tp-100) REVERT: B 576 ARG cc_start: 0.8551 (mtm180) cc_final: 0.8189 (ttt180) REVERT: B 588 PHE cc_start: 0.8947 (m-80) cc_final: 0.8647 (m-80) REVERT: B 598 LEU cc_start: 0.9568 (mt) cc_final: 0.9017 (mt) REVERT: B 619 TYR cc_start: 0.7929 (t80) cc_final: 0.7718 (t80) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.4201 time to fit residues: 34.9328 Evaluate side-chains 45 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.199 Evaluate side-chains 70 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 ASN cc_start: 0.8881 (t0) cc_final: 0.8657 (t0) REVERT: A 84 VAL cc_start: 0.8884 (t) cc_final: 0.8237 (t) REVERT: A 184 HIS cc_start: 0.8971 (m90) cc_final: 0.8447 (m-70) REVERT: A 212 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7656 (mmtm) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.3604 time to fit residues: 29.0799 Evaluate side-chains 52 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.365 Evaluate side-chains 55 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 143 LEU cc_start: 0.9468 (tp) cc_final: 0.9063 (pp) REVERT: G 204 TYR cc_start: 0.8539 (m-80) cc_final: 0.7956 (m-80) REVERT: G 219 PHE cc_start: 0.8743 (m-80) cc_final: 0.7782 (m-80) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.5069 time to fit residues: 30.1114 Evaluate side-chains 34 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.269 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0026 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 9.9990 chunk 163 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 0.0670 chunk 110 optimal weight: 0.0470 chunk 87 optimal weight: 10.0000 chunk 169 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 126 optimal weight: 0.0060 chunk 196 optimal weight: 0.9980 overall best weight: 0.4032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 614 ASN B 617 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 HIS Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.053226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.052830 restraints weight = 510.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.053072 restraints weight = 105.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.053169 restraints weight = 31.660| |-----------------------------------------------------------------------------| r_work (final): 0.2832 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.071847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056353 restraints weight = 22429.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.059683 restraints weight = 12980.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.062475 restraints weight = 8463.916| |-----------------------------------------------------------------------------| r_work (final): 0.3372 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.057603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.044983 restraints weight = 42719.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.047998 restraints weight = 21614.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.050345 restraints weight = 12958.878| |-----------------------------------------------------------------------------| r_work (final): 0.3221 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.063793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.049323 restraints weight = 35498.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.053054 restraints weight = 20310.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.055909 restraints weight = 12668.398| |-----------------------------------------------------------------------------| r_work (final): 0.3573 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.040629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.037789 restraints weight = 692.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.038225 restraints weight = 436.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.038509 restraints weight = 325.670| |-----------------------------------------------------------------------------| r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 17997 Z= 0.226 Angle : 0.911 14.071 24459 Z= 0.486 Chirality : 0.049 0.257 2694 Planarity : 0.015 0.426 3132 Dihedral : 11.027 73.504 3075 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.49 % Allowed : 2.27 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.14), residues: 2172 helix: -0.85 (0.26), residues: 339 sheet: -2.78 (0.19), residues: 495 loop : -2.86 (0.13), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 153 HIS 0.019 0.002 HIS A 32 PHE 0.019 0.002 PHE I 154 TYR 0.025 0.002 TYR C 102 ARG 0.023 0.002 ARG D 575 Details of bonding type rmsd link_NAG-ASN : bond 0.00778 ( 24) link_NAG-ASN : angle 2.63685 ( 72) link_BETA1-4 : bond 0.01545 ( 9) link_BETA1-4 : angle 4.49603 ( 27) hydrogen bonds : bond 0.08197 ( 654) hydrogen bonds : angle 8.53770 ( 1845) SS BOND : bond 0.01829 ( 21) SS BOND : angle 1.41146 ( 42) covalent geometry : bond 0.00486 (17943) covalent geometry : angle 0.88815 (24318) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 63 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.9789 (tp40) cc_final: 0.9563 (tp-100) REVERT: B 576 ARG cc_start: 0.8701 (mtm180) cc_final: 0.8465 (ttt180) REVERT: B 619 TYR cc_start: 0.9142 (t80) cc_final: 0.8900 (t80) REVERT: B 620 GLU cc_start: 0.9736 (mm-30) cc_final: 0.9520 (mm-30) REVERT: B 623 LYS cc_start: 0.9851 (tttt) cc_final: 0.9588 (tppt) REVERT: B 662 TYR cc_start: 0.9229 (m-80) cc_final: 0.8939 (m-80) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 0.3279 time to fit residues: 22.0930 Evaluate side-chains 45 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.224 Evaluate side-chains 57 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 ASP cc_start: 0.9284 (t0) cc_final: 0.8969 (t0) REVERT: C 85 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8471 (mp0) REVERT: C 104 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6879 (mp0) REVERT: C 204 VAL cc_start: 0.9483 (m) cc_final: 0.9205 (m) REVERT: C 209 TYR cc_start: 0.9392 (t80) cc_final: 0.9187 (t80) REVERT: C 231 ASN cc_start: 0.9724 (m-40) cc_final: 0.9379 (t0) outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 0.2010 time to fit residues: 14.6661 Evaluate side-chains 42 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.367 Evaluate side-chains 39 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 204 TYR cc_start: 0.8905 (m-80) cc_final: 0.8253 (m-80) REVERT: H 219 PHE cc_start: 0.9157 (m-80) cc_final: 0.8288 (m-80) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.6752 time to fit residues: 27.9649 Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.246 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0027 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 122 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 82 optimal weight: 0.0970 chunk 71 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 84 optimal weight: 0.8980 chunk 87 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.053390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.053009 restraints weight = 465.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.053224 restraints weight = 98.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.053320 restraints weight = 31.520| |-----------------------------------------------------------------------------| r_work (final): 0.2836 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.079657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.066985 restraints weight = 26871.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.070303 restraints weight = 15846.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.072927 restraints weight = 10186.472| |-----------------------------------------------------------------------------| r_work (final): 0.3624 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.057723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.045426 restraints weight = 45570.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.048323 restraints weight = 22755.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.050620 restraints weight = 13617.389| |-----------------------------------------------------------------------------| r_work (final): 0.3218 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.064035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.050489 restraints weight = 38448.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.054116 restraints weight = 21686.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.056860 restraints weight = 13472.427| |-----------------------------------------------------------------------------| r_work (final): 0.3460 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2367 r_free = 0.2367 target = 0.040242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2347 r_free = 0.2347 target = 0.037388 restraints weight = 527.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2349 r_free = 0.2349 target = 0.037963 restraints weight = 319.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2351 r_free = 0.2351 target = 0.038251 restraints weight = 235.498| |-----------------------------------------------------------------------------| r_work (final): 0.2376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.170 17997 Z= 0.311 Angle : 1.019 13.735 24459 Z= 0.544 Chirality : 0.053 0.323 2694 Planarity : 0.016 0.407 3132 Dihedral : 10.781 72.150 3075 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 0.16 % Allowed : 0.65 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.15), residues: 2172 helix: -1.11 (0.26), residues: 336 sheet: -2.81 (0.18), residues: 561 loop : -2.85 (0.13), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP C 153 HIS 0.016 0.003 HIS C 32 PHE 0.025 0.002 PHE A 118 TYR 0.078 0.004 TYR C 195 ARG 0.041 0.002 ARG B 606 Details of bonding type rmsd link_NAG-ASN : bond 0.00780 ( 24) link_NAG-ASN : angle 2.58615 ( 72) link_BETA1-4 : bond 0.01239 ( 9) link_BETA1-4 : angle 3.77947 ( 27) hydrogen bonds : bond 0.08117 ( 654) hydrogen bonds : angle 8.53243 ( 1845) SS BOND : bond 0.02174 ( 21) SS BOND : angle 1.72353 ( 42) covalent geometry : bond 0.00747 (17943) covalent geometry : angle 1.00227 (24318) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3702 Ramachandran restraints generated. 1851 Oldfield, 0 Emsley, 1851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0032 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 58 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.9773 (tp40) cc_final: 0.9504 (tp-100) REVERT: B 576 ARG cc_start: 0.8616 (mtm180) cc_final: 0.8321 (ttt180) REVERT: B 595 ASN cc_start: 0.9660 (m-40) cc_final: 0.9396 (m-40) REVERT: B 619 TYR cc_start: 0.9123 (t80) cc_final: 0.8876 (t80) REVERT: B 623 LYS cc_start: 0.9847 (tttt) cc_final: 0.9578 (tppt) REVERT: B 662 TYR cc_start: 0.9062 (m-80) cc_final: 0.8830 (m-80) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.3117 time to fit residues: 20.1657 Evaluate side-chains 42 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.237 Evaluate side-chains 47 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 ASP cc_start: 0.9315 (t0) cc_final: 0.9082 (t0) REVERT: C 85 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8553 (mp0) REVERT: C 204 VAL cc_start: 0.9560 (m) cc_final: 0.9188 (m) REVERT: C 209 TYR cc_start: 0.9403 (t80) cc_final: 0.9181 (t80) REVERT: C 231 ASN cc_start: 0.9739 (m-40) cc_final: 0.9455 (t0) REVERT: C 264 PHE cc_start: 0.8971 (p90) cc_final: 0.8733 (p90) outliers start: 1 outliers final: 1 residues processed: 47 average time/residue: 0.2600 time to fit residues: 15.4168 Evaluate side-chains 41 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.394 Evaluate side-chains 36 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 204 TYR cc_start: 0.8917 (m-80) cc_final: 0.8285 (m-80) REVERT: H 219 PHE cc_start: 0.9205 (m-80) cc_final: 0.8340 (m-80) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.7404 time to fit residues: 28.3312 Evaluate side-chains 28 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.291 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0034 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 48 optimal weight: 50.0000 chunk 123 optimal weight: 0.0000 chunk 53 optimal weight: 8.9990 chunk 191 optimal weight: 0.3980 chunk 62 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 158 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 108 GLN C 183 HIS C 296 GLN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 198 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.052707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.052365 restraints weight = 471.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.052559 restraints weight = 100.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.052659 restraints weight = 33.968| |-----------------------------------------------------------------------------| r_work (final): 0.2607 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.069785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.055705 restraints weight = 21387.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.058889 restraints weight = 11570.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.061525 restraints weight = 7202.493| |-----------------------------------------------------------------------------| r_work (final): 0.3360 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.058032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.046740 restraints weight = 46028.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.049604 restraints weight = 22673.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.051740 restraints weight = 13262.665| |-----------------------------------------------------------------------------| r_work (final): 0.3229 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.098607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.087638 restraints weight = 52835.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.089885 restraints weight = 26542.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.091204 restraints weight = 14643.007| |-----------------------------------------------------------------------------| r_work (final): 0.3665 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2205 r_free = 0.2205 target = 0.032741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2184 r_free = 0.2184 target = 0.030659 restraints weight = 757.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2189 r_free = 0.2189 target = 0.031018 restraints weight = 452.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2191 r_free = 0.2191 target = 0.031253 restraints weight = 329.830| |-----------------------------------------------------------------------------| r_work (final): 0.2172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17997 Z= 0.219 Angle : 0.915 18.534 24459 Z= 0.483 Chirality : 0.051 0.382 2694 Planarity : 0.013 0.330 3132 Dihedral : 9.835 51.721 3075 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 0.16 % Allowed : 1.62 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.15), residues: 2172 helix: -1.22 (0.25), residues: 339 sheet: -2.64 (0.19), residues: 525 loop : -2.99 (0.13), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 153 HIS 0.014 0.002 HIS C 32 PHE 0.028 0.002 PHE C 118 TYR 0.045 0.003 TYR C 95 ARG 0.014 0.001 ARG C 311 Details of bonding type rmsd link_NAG-ASN : bond 0.00824 ( 24) link_NAG-ASN : angle 2.61771 ( 72) link_BETA1-4 : bond 0.00963 ( 9) link_BETA1-4 : angle 3.49868 ( 27) hydrogen bonds : bond 0.06801 ( 654) hydrogen bonds : angle 8.16332 ( 1845) SS BOND : bond 0.01837 ( 21) SS BOND : angle 1.47114 ( 42) covalent geometry : bond 0.00501 (17943) covalent geometry : angle 0.89723 (24318) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3238 Ramachandran restraints generated. 1619 Oldfield, 0 Emsley, 1619 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 pdbres="ILE B 673 " Cannot extract axes_and_atoms_to_rotate: n_branches <= 2, n_branches: 8 Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 92 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0022 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Evaluate side-chains 59 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 542 GLN cc_start: 0.9788 (tp40) cc_final: 0.9568 (tp-100) REVERT: B 595 ASN cc_start: 0.9525 (m-40) cc_final: 0.9214 (p0) REVERT: B 619 TYR cc_start: 0.9250 (t80) cc_final: 0.9039 (t80) REVERT: B 662 TYR cc_start: 0.9187 (m-80) cc_final: 0.8940 (m-80) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.2977 time to fit residues: 19.4452 Evaluate side-chains 43 residues out of total 149 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.232 Evaluate side-chains 43 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 ASP cc_start: 0.9376 (t0) cc_final: 0.9099 (t0) REVERT: C 85 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8476 (mp0) REVERT: C 204 VAL cc_start: 0.9533 (m) cc_final: 0.9210 (m) REVERT: C 231 ASN cc_start: 0.9655 (m-40) cc_final: 0.9200 (t0) REVERT: C 264 PHE cc_start: 0.8936 (p90) cc_final: 0.8699 (p90) outliers start: 1 outliers final: 1 residues processed: 43 average time/residue: 0.2217 time to fit residues: 12.1308 Evaluate side-chains 35 residues out of total 283 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.409 Evaluate side-chains 38 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 204 TYR cc_start: 0.9230 (m-80) cc_final: 0.8847 (m-80) REVERT: G 219 PHE cc_start: 0.9269 (m-80) cc_final: 0.8431 (m-80) REVERT: G 239 MET cc_start: 0.9590 (tpp) cc_final: 0.9166 (tpp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.6419 time to fit residues: 26.0031 Evaluate side-chains 30 residues out of total 186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.270 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0029 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.3295 > 50: distance: 0 - 1: 13.519 distance: 0 - 6: 7.599 distance: 1 - 2: 18.419 distance: 1 - 4: 16.466 distance: 1 - 7: 6.509 distance: 2 - 3: 45.922 distance: 2 - 11: 33.755 distance: 4 - 5: 16.722 distance: 4 - 8: 22.603 distance: 4 - 9: 31.053 distance: 5 - 10: 42.590 distance: 11 - 12: 16.524 distance: 11 - 18: 40.445 distance: 12 - 13: 10.764 distance: 12 - 15: 30.556 distance: 12 - 19: 17.143 distance: 13 - 14: 28.229 distance: 13 - 27: 28.922 distance: 15 - 16: 26.893 distance: 15 - 17: 33.832 distance: 15 - 20: 36.930 distance: 16 - 21: 26.859 distance: 16 - 22: 12.456 distance: 16 - 23: 13.387 distance: 17 - 24: 54.140 distance: 17 - 25: 51.442 distance: 17 - 26: 40.753 distance: 27 - 28: 37.025 distance: 27 - 35: 40.474 distance: 28 - 29: 40.134 distance: 28 - 31: 14.753 distance: 28 - 36: 23.166 distance: 29 - 30: 32.061 distance: 29 - 41: 31.571 distance: 31 - 32: 42.536 distance: 31 - 37: 40.702 distance: 31 - 38: 34.623 distance: 32 - 33: 24.514 distance: 32 - 34: 27.608 distance: 34 - 39: 32.220 distance: 34 - 40: 24.935 distance: 41 - 49: 17.970 distance: 42 - 43: 12.863 distance: 42 - 45: 5.457 distance: 42 - 50: 7.680 distance: 43 - 44: 13.543 distance: 43 - 60: 8.676 distance: 45 - 46: 12.309 distance: 45 - 51: 7.249 distance: 45 - 52: 8.414 distance: 46 - 48: 5.072 distance: 46 - 53: 8.451 distance: 47 - 54: 9.509 distance: 47 - 55: 8.627 distance: 47 - 56: 9.809 distance: 48 - 57: 10.727 distance: 48 - 58: 21.413 distance: 48 - 59: 22.690 distance: 60 - 61: 8.793 distance: 60 - 68: 7.229 distance: 61 - 62: 13.963 distance: 61 - 64: 19.060 distance: 61 - 69: 7.701 distance: 62 - 63: 13.439 distance: 62 - 79: 32.429 distance: 64 - 65: 14.782 distance: 64 - 70: 26.709 distance: 64 - 71: 23.701 distance: 65 - 66: 37.268 distance: 65 - 67: 13.587 distance: 65 - 72: 8.843 distance: 66 - 73: 43.484 distance: 66 - 74: 45.975 distance: 66 - 75: 44.753 distance: 67 - 76: 20.208 distance: 67 - 77: 18.391 distance: 67 - 78: 6.741 distance: 79 - 80: 15.442 distance: 79 - 88: 17.931 distance: 80 - 81: 12.243 distance: 80 - 83: 10.858 distance: 80 - 89: 9.272 distance: 81 - 82: 10.199 distance: 81 - 94: 16.690 distance: 83 - 84: 23.108 distance: 83 - 90: 12.995 distance: 83 - 91: 7.817 distance: 84 - 85: 17.333 distance: 84 - 92: 13.054 distance: 85 - 86: 18.006 distance: 85 - 87: 37.110 distance: 94 - 95: 6.934 distance: 94 - 102: 12.828 distance: 95 - 96: 19.482 distance: 95 - 98: 7.363 distance: 95 - 103: 6.931 distance: 96 - 97: 10.201 distance: 96 - 106: 39.205 distance: 98 - 99: 11.021 distance: 98 - 104: 12.065 distance: 98 - 105: 11.274 distance: 99 - 100: 4.408 distance: 106 - 107: 9.353 distance: 106 - 112: 8.019 distance: 107 - 108: 6.111 distance: 107 - 110: 14.646 distance: 107 - 113: 13.929 distance: 108 - 109: 11.337 distance: 108 - 117: 29.581 distance: 110 - 111: 14.498 distance: 110 - 114: 17.970 distance: 110 - 115: 20.320 distance: 111 - 116: 33.262 distance: 117 - 118: 10.004 distance: 117 - 127: 9.749 distance: 118 - 119: 9.190 distance: 118 - 121: 15.964 distance: 118 - 128: 7.798 distance: 119 - 120: 11.188 distance: 119 - 134: 7.506 distance: 121 - 122: 3.728 distance: 121 - 129: 3.315 distance: 121 - 130: 7.435 distance: 122 - 123: 3.034 distance: 122 - 124: 5.781 distance: 123 - 125: 3.827 distance: 124 - 126: 3.175 distance: 124 - 131: 4.438 distance: 125 - 126: 9.058 distance: 126 - 133: 3.016 distance: 134 - 135: 5.384 distance: 134 - 142: 6.043 distance: 135 - 143: 5.900 distance: 136 - 137: 4.615 distance: 138 - 139: 4.222 distance: 138 - 145: 3.681 distance: 139 - 141: 3.175